10:00a – 11:30p
Project 2
- see notes
Chromatin Project
New Probes making
- L3: B02 – B09
- L2: F03, F04, F05, F06, F07. L3: F09, F10, F11 (all 2 color),
- running QPCR (try 2)
- over-ran a little bit, amplification happens quite rapidly (less than 8 minutes) between cycles 25 and 30.
- PCR cleanup of all samples
- Setup T7 IVT reactions, B02-B09 20 uL reactions (renumbered as 1-8). F03-F11 (renumbered as 9-16) as 40 uL reactions (want more RNA to do more RT reactions)
Bogdan and black chromatin
STORM
- Finished imaging L3F04-p1-A647 + L3F03-p3-A750
- Start imaging L3F02-p1-A647 + L3F03-p3-A750
Chromatin Analysis
- E01 and E02 samples seriously under-stained / under-sampled / too-short images. Apparent domains are large, but sampling density is insufficient to resolve details and keep domain connected. less than 1000 localization for many of these 250 and 175 kb (respectively) regions.
- Analyzed E06
- Analyzed E07
- Analyzed E10 up to image 25 (50 spots)
matlab-storm
- still trouble-shooting
- fixed some bugs in parameter passing from GUI-popup window to main analysis function
- Warps do not seem to be getting applied to data, points aren’t moving.
- My ‘translation rotation’ function for ‘WarpPoints’ seems to be in error.